5,879 research outputs found
Accurate Pulmonary Nodule Detection in Computed Tomography Images Using Deep Convolutional Neural Networks
Early detection of pulmonary cancer is the most promising way to enhance a
patient's chance for survival. Accurate pulmonary nodule detection in computed
tomography (CT) images is a crucial step in diagnosing pulmonary cancer. In
this paper, inspired by the successful use of deep convolutional neural
networks (DCNNs) in natural image recognition, we propose a novel pulmonary
nodule detection approach based on DCNNs. We first introduce a deconvolutional
structure to Faster Region-based Convolutional Neural Network (Faster R-CNN)
for candidate detection on axial slices. Then, a three-dimensional DCNN is
presented for the subsequent false positive reduction. Experimental results of
the LUng Nodule Analysis 2016 (LUNA16) Challenge demonstrate the superior
detection performance of the proposed approach on nodule detection(average
FROC-score of 0.891, ranking the 1st place over all submitted results).Comment: MICCAI 2017 accepte
Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution
The effect of asymmetry in the transbilayer lipid distribution on the
dynamics of phase separation in fluid vesicles is investigated numerically for
the first time. This asymmetry is shown to set a spontaneous curvature for the
domains that alter the morphology and dynamics considerably. For moderate
tension, the domains are capped and the spontaneous curvature leads to
anomalously slow dynamics, as compared to the case of symmetric bilayers. In
contrast, in the limiting cases of high and low tensions, the dynamics proceeds
towards full phase separation.Comment: 4 pages, 5 figure
Are stress-free membranes really 'tensionless'?
In recent years it has been argued that the tension parameter driving the
fluctuations of fluid membranes, differs from the imposed lateral stress, the
'frame tension'. In particular, stress-free membranes were predicted to have a
residual fluctuation tension. In the present paper, this argument is
reconsidered and shown to be inherently inconsistent -- in the sense that a
linearized theory, the Monge model, is used to predict a nonlinear effect.
Furthermore, numerical simulations of one-dimensional stiff membranes are
presented which clearly demonstrate, first, that the internal 'intrinsic'
stress in membranes indeed differs from the frame tension as conjectured, but
second, that the fluctuations are nevertheless driven by the frame tension.
With this assumption, the predictions of the Monge model agree excellently with
the simulation data for stiffness and tension values spanning several orders of
magnitude
Ergodic and Nonergodic Anomalous Diffusion in Coupled Stochastic Processes
Inspired by problems in biochemical kinetics, we study statistical properties
of an overdamped Langevin process whose friction coefficient depends on the
state of a similar, unobserved process. Integrating out the latter, we derive
the long time behaviour of the mean square displacement. Anomalous diffusion is
found. Since the diffusion exponent can not be predicted using a simple scaling
argument, anomalous scaling appears as well. We also find that the coupling can
lead to ergodic or non-ergodic behaviour of the studied process. We compare our
theoretical predictions with numerical simulations and find an excellent
agreement. The findings caution against treating biochemical systems coupled
with unobserved dynamical degrees of freedom by means of standard, diffusive
Langevin descriptions
Model for the unidirectional motion of a dynein molecule
Cytoplasmic dyneins transport cellular organelles by moving on a microtubule
filament. It has been found recently that depending on the applied force and
the concentration of the adenosine triphosphate (ATP) molecules, dynein's step
size varies. Based on these studies, we propose a simple model for dynein's
unidirectional motion taking into account the variations in its step size. We
study how the average velocity and the relative dispersion in the displacement
vary with the applied load. The model is amenable to further extensions by
inclusion of details associated with the structure and the processivity of the
molecule.Comment: 10 pages, 5 figure
Membrane fluctuations near a plane rigid surface
We use analytical calculations and Monte Carlo simulations to determine the
thermal fluctuation spectrum of a membrane patch of a few tens of nanometer in
size, whose corners are located at a fixed distance above a plane rigid
surface. Our analysis shows that the surface influence on the bilayer
fluctuations can be effectively described in terms of a uniform confining
potential that grows quadratically with the height of the membrane relative
to the surface: . The strength of the harmonic
confining potential vanishes when the corners of the membrane patch are placed
directly on the surface (), and achieves its maximum value when is of
the order of a few nanometers. However, even at maximum strength the
confinement effect is quite small and has noticeable impact only on the
amplitude of the largest bending mode.Comment: Accepted for publication in Phys. Rev.
Mean encounter times for cell adhesion in hydrodynamic flow: analytical progress by dimensional reduction
For a cell moving in hydrodynamic flow above a wall, translational and
rotational degrees of freedom are coupled by the Stokes equation. In addition,
there is a close coupling of convection and diffusion due to the
position-dependent mobility. These couplings render calculation of the mean
encounter time between cell surface receptors and ligands on the substrate very
difficult. Here we show for a two-dimensional model system how analytical
progress can be achieved by treating motion in the vertical direction by an
effective reaction term in the mean first passage time equation for the
rotational degree of freedom. The strength of this reaction term can either be
estimated from equilibrium considerations or used as a fit parameter. Our
analytical results are confirmed by computer simulations and allow to assess
the relative roles of convection and diffusion for different scaling regimes of
interest.Comment: Reftex, postscript figures include
Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers
A systematic investigation of the phase separation dynamics in self-assembled
multi-component bilayer fluid vesicles and open membranes is presented. We use
large-scale dissipative particle dynamics to explicitly account for solvent,
thereby allowing for numerical investigation of the effects of hydrodynamics
and area-to-volume constraints. In the case of asymmetric lipid composition, we
observed regimes corresponding to coalescence of flat patches, budding,
vesiculation and coalescence of caps. The area-to-volume constraint and
hydrodynamics have a strong influence on these regimes and the crossovers
between them. In the case of symmetric mixtures, irrespective of the
area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The
same exponent is also found in the case of open membranes with symmetric
composition
Steady-state MreB helices inside bacteria: dynamics without motors
Within individual bacteria, we combine force-dependent polymerization
dynamics of individual MreB protofilaments with an elastic model of
protofilament bundles buckled into helical configurations. We use variational
techniques and stochastic simulations to relate the pitch of the MreB helix,
the total abundance of MreB, and the number of protofilaments. By comparing our
simulations with mean-field calculations, we find that stochastic fluctuations
are significant. We examine the quasi-static evolution of the helical pitch
with cell growth, as well as timescales of helix turnover and denovo
establishment. We find that while the body of a polarized MreB helix treadmills
towards its slow-growing end, the fast-growing tips of laterally associated
protofilaments move towards the opposite fast-growing end of the MreB helix.
This offers a possible mechanism for targeted polar localization without
cytoplasmic motor proteins.Comment: 7 figures, 1 tabl
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